Package index • gp3bayes

Package overview

gp3bayes gp3bayes-package: gp3bayes: Contract-First Bayesian Workflows for Hierarchical Behavioural Data

Model contracts

create_model_contract(): Create an Approved Bayesian Model Contract

Readiness audits

audit_model_readiness(): Audit Data Readiness for an Approved Model Contract

Model specifications

build_model_formula(): Build an Approved Model Formula
create_prior_specification(): Create a Backend-Independent Prior Specification
validate_prior_specification(): Validate a Prior Specification
create_model_specification(): Create a Complete Model Specification

Binary workflow foundation

simulate_hierarchical_binary_data(): Simulate Hierarchical Binary Data
prepare_hierarchical_binary_data(): Prepare Hierarchical Binary Data
specify_binary_model(): Specify a Backend-Independent Binary Model
check_binary_prior_predictive(): Check Binary Prior Predictive Behaviour

Binary model fitting

translate_binary_model_to_brms(): Translate a Binary Model Specification to brms
fit_binary_model(): Fit an Approved Hierarchical Binary Model

Binary posterior validation

diagnose_binary_fit(): Diagnose a Fitted Binary Model
summarise_binary_posterior(): Summarise a Binary Posterior
check_binary_posterior_predictive(): Check Binary Posterior Predictive Behaviour
assess_binary_prior_sensitivity(): Assess Binary Prior Sensitivity
run_binary_recovery(): Run Binary Parameter Recovery
create_binary_model_report(): Create a Structured Binary Model Report
plot_sampling_diagnostics(): Plot Sampling Diagnostics

Lognormal duration workflow

simulate_hierarchical_duration_data(): Simulate Hierarchical Lognormal Duration Data
prepare_hierarchical_duration_data(): Prepare Hierarchical Duration Data
specify_duration_model(): Specify a Backend-Independent Duration Model
check_duration_prior_predictive(): Check Duration Prior Predictive Behaviour
translate_duration_model_to_brms(): Translate a Duration Model Specification to brms
fit_duration_model(): Fit an Approved Hierarchical Lognormal Duration Model

Duration posterior validation

diagnose_duration_fit(): Diagnose a Fitted Duration Model
summarise_duration_posterior(): Summarise a Duration Posterior
check_duration_posterior_predictive(): Check Duration Posterior Predictive Behaviour
assess_duration_prior_sensitivity(): Assess Duration Prior Sensitivity
run_duration_recovery(): Run Duration Parameter Recovery
create_duration_model_report(): Create a Structured Duration Model Report

Advanced optional workflows

bayesian_backend_capabilities(): Report Optional Bayesian Backend Capabilities
check_cmdstan_backend(): Check the CmdStanR Backend
specify_binary_model_with_interaction_prior(): Specify a Binary Model with a Separate Interaction Prior
specify_duration_model_with_interaction_prior(): Specify a Duration Model with a Separate Interaction Prior
interaction_prior_summary(): Summarise Separate Interaction Prior Metadata
translate_binary_model_with_interaction_prior(): Translate an Advanced Binary Specification to brms
translate_duration_model_with_interaction_prior(): Translate an Advanced Duration Specification to brms
fit_binary_model_backend() fit_binary_model_cmdstanr(): Fit a Binary Model with a Selected Full-MCMC Backend
fit_duration_model_backend() fit_duration_model_cmdstanr(): Fit a Duration Model with a Selected Full-MCMC Backend
detect_binary_separation(): Detect Separation in the Binary Fixed-Effects Screen
compute_psis_loo(): Compute PSIS-LOO for a gp3bayes Fit
compute_psis_loo_from_log_lik(): Compute PSIS-LOO from a Log-Likelihood Matrix
identify_loo_influential_observations(): Identify Influential PSIS-LOO Observations
compare_psis_loo(): Compare Models with PSIS-LOO
compute_loo_model_weights(): Compute LOO Model-Averaging Weights
assess_powerscaled_sensitivity(): Assess Power-Scaled Prior and Likelihood Sensitivity
powerscale_sequence_for_fit(): Create a Power-Scaling Sequence
simulate_binary_pathology(): Simulate a Dedicated Binary Pathology Scenario
simulate_duration_pathology(): Simulate a Dedicated Duration Pathology Scenario
evaluate_pathological_simulation(): Evaluate a Pathological Simulation Against the Contract Gate
create_brms_sbc_plan(): Create a brms-Based Simulation-Based Calibration Plan
create_custom_sbc_plan(): Create an Expert Custom SBC Plan
run_sbc_plan(): Run a Simulation-Based Calibration Plan
summarise_sbc_result(): Summarise an SBC Result

Specification closure

summarise_condition_balance(): Summarise Overall Condition Balance
summarise_binary_group_variation(): Summarise Binary Outcome Variation Within Groups
identify_identifier_like_predictors(): Identify Identifier-Like Numeric Predictors
review_duration_extremes(): Review Extreme Positive Durations Without Deleting Them
audit_duration_boundaries(): Audit Duration Range and Censoring Boundaries
audit_model_readiness_strict(): Run a Strict Model-Readiness Audit
plot(<gp3bayes_strict_readiness_audit>): Plot a Strict Readiness Audit
create_transformation_recipe(): Create a Reusable Transformation Recipe
apply_transformation_recipe(): Apply a Recorded Transformation Recipe
invert_transformation_recipe(): Invert a Recorded Transformation Recipe
validate_transformation_replay(): Validate Exact Transformation Replay
estimate_standardized_probability_contrast(): Estimate a Design-Standardised Binary Probability Contrast
estimate_standardized_duration_estimands(): Estimate Design-Standardised Duration Estimands
summarise_estimand_draws(): Summarise Posterior Estimand Draws
create_random_slope_sensitivity_plan(): Create a Random-Slope Sensitivity Plan
run_random_slope_sensitivity(): Run Random-Intercept versus Random-Slope Sensitivity
create_group_deletion_sensitivity_plan(): Create a Group-Deletion Sensitivity Plan
run_group_deletion_sensitivity(): Run a Group-Deletion Sensitivity Plan
compare_estimand_sensitivity(): Compare Estimand Sensitivity Across Alternative Fits
audit_estimand_invariance(): Audit Estimand Invariance Against a Declared Tolerance
create_contrast_coding_sensitivity_specification(): Create a Contrast-Coding Sensitivity Specification
create_predictor_scaling_sensitivity_specification(): Create a Predictor-Scaling Sensitivity Specification
create_duration_unit_sensitivity_specification(): Create a Duration-Unit Sensitivity Specification
audit_duration_unit_invariance(): Audit Duration-Unit Invariance
check_binary_ppc_details(): Run Detailed Binary Posterior Predictive Checks
check_duration_ppc_details(): Run Detailed Duration Posterior Predictive Checks
compute_kfold_cv(): Compute Governed Exact K-Fold Cross-Validation
plot(<gp3bayes_kfold_cv>): Plot Governed Exact K-Fold Results
gp3bayes_specification_traceability(): Specification-Closure Traceability Matrix

Stable 0.2.0 workflow API

validate_gp3bayes_object(): Validate a gp3bayes Object
diagnose_model_fit(): Diagnose an Approved gp3bayes Fit
summarise_model_posterior(): Summarise an Approved gp3bayes Posterior
check_model_ppc(): Check Posterior Predictive Behaviour
estimate_model_estimands(): Estimate the Approved Primary Estimands
model_workflow_status(): Summarise Workflow Stage Completion

Reproducibility and manifests

create_analysis_manifest(): Create an Analysis Manifest
validate_analysis_manifest(): Validate an Analysis Manifest
freeze_analysis_manifest(): Freeze an Analysis Manifest
read_analysis_manifest(): Read a Frozen Analysis Manifest
compare_analysis_manifests(): Compare Analysis Manifests
analysis_manifest_table(): Summarise Manifest Components
write_reproducibility_report(): Write a Reproducibility Report

Pre-fit design support

audit_missingness_structure(): Audit Missingness Structure Before Model Fitting
audit_fixed_effect_design(): Audit the Fixed-Effects Design Matrix
audit_random_effects_support(): Audit Random-Effects Support
audit_design_support(): Audit Overall Design Support
preflight_model_specification(): Preflight an Approved Model Specification

Unified sensitivity and evidence

create_sensitivity_suite_plan(): Create a Sensitivity Suite Plan
run_sensitivity_suite(): Run a Unified Sensitivity Suite
summarise_sensitivity_suite(): Summarise a Sensitivity Suite
collect_model_evidence(): Collect Model Evidence Without Declaring Model Adequacy
create_model_evidence_report(): Create a Model Evidence Report

Backend reliability and compatibility

backend_capabilities(): Report Bayesian Backend Capabilities
validate_backend_environment(): Validate a Bayesian Backend Environment
audit_backend_parity(): Audit Posterior Parity Across rstan and cmdstanr
capture_gp3bayes_schema(): Capture the Structural Schema of a gp3bayes Object
compare_gp3bayes_schemas(): Compare gp3bayes Object Schemas
validate_gp3bayes_schema(): Validate an Object Against a Frozen gp3bayes Schema
freeze_gp3bayes_schema(): Freeze a gp3bayes Object Schema
read_gp3bayes_schema(): Read a Frozen gp3bayes Object Schema

Post-fit exploration and prediction

extract_posterior_draws(): Extract Posterior Draws from a gp3bayes Fit
extract_sampler_diagnostics(): Extract NUTS Sampler Diagnostics
extract_log_likelihood(): Extract Pointwise Log-Likelihood Draws
posterior_interval_table(): Posterior Interval Table
posterior_probability_table(): Posterior Direction and ROPE Probability Table
posterior_correlation_table(): Posterior Correlation Table
mcmc_diagnostic_table(): Modern MCMC Diagnostic Table
sampler_diagnostic_table(): Summarise NUTS Sampler Diagnostics
identify_mcmc_issues(): Identify MCMC Diagnostic Flags
summarise_mcmc_quality(): Summarise MCMC Quality Evidence
group_effect_table(): Group-Level Effect Table
variance_component_table(): Variance-Component Posterior Table
create_prediction_grid(): Create a Governed Prediction Grid
audit_prediction_support(): Audit Prediction Support
prediction_support_table(): Prediction-Support Table
predict_model(): Posterior Prediction for Approved gp3bayes Models
predict_binary_probability(): Binary Event-Probability Predictions
predict_duration(): Duration Predictions
extract_expected_predictions(): Extract Expected Posterior Predictions
extract_posterior_predictions(): Extract Posterior Predictive Draws
extract_linear_predictions(): Extract Linear-Predictor Draws
prediction_table(): Prediction Summary Table
prediction_contrast(): Posterior Prediction Contrast
prediction_exceedance_probability(): Posterior Exceedance Probabilities
prediction_uncertainty_decomposition(): Decompose Prediction Uncertainty Descriptively
grouped_prediction_check(): Grouped Posterior Predictive Check
predictive_residuals(): Posterior Predictive Residuals
binary_prediction_scores(): Binary Prediction Scores
binary_threshold_metrics(): Binary Threshold-Metric Curve
binary_calibration_table(): Binary Calibration Table
duration_prediction_scores(): Duration Prediction Scores
duration_quantile_calibration(): Duration Quantile Calibration
duration_pit_table(): Duration Probability-Integral-Transform Table
predictive_coverage_table(): Posterior Predictive Coverage Table
posterior_predictive_summary_table(): Posterior Predictive Summary Table

LOO tables and publication graphics

loo_diagnostic_table(): LOO Diagnostic Table
loo_summary_table(): LOO Summary Table
model_comparison_table(): LOO Model-Comparison Table
model_weights_table(): LOO Model-Weight Table
theme_gp3bayes(): gp3bayes Publication Theme
plot_posterior_intervals(): Posterior Interval Plot
plot_posterior_areas(): Posterior Area Plot
plot_posterior_density(): Posterior Density Plot
plot_posterior_correlations(): Posterior Correlation Plot
plot_posterior_pairs(): Posterior Pairs Plot
plot_rank_diagnostics(): Rank-Diagnostic Plot
plot_autocorrelation(): Autocorrelation Diagnostic Plot
plot_mcmc_quality(): MCMC Review-Flag Plot
plot_sampler_diagnostics(): Sampler-Diagnostic Plot
plot_estimand_intervals(): Estimand Interval Plot
plot_prediction_intervals(): Prediction-Interval Plot
plot_binary_calibration(): Binary Calibration Plot
plot_binary_threshold_metrics(): Binary Threshold-Metric Plot
plot_duration_quantile_calibration(): Duration Quantile-Calibration Plot
plot_duration_pit(): Duration PIT Plot
plot_exceedance_probability(): Prediction Exceedance-Probability Plot
plot_predictive_coverage(): Predictive-Coverage Plot
plot_predictive_residuals(): Predictive-Residual Plot
plot_prediction_support(): Prediction-Support Plot
plot_uncertainty_decomposition(): Prediction-Uncertainty Plot
plot_grouped_prediction_check(): Grouped Posterior Predictive Plot
plot_group_effects(): Group-Effect Plot
plot_variance_components(): Variance-Component Plot
plot_loo_influence(): LOO Influence Plot
plot_model_comparison(): LOO Model-Comparison Plot
plot_model_weights(): LOO Model-Weight Plot
create_figure_set(): Create a Named Figure Set
save_figure_set(): Save a Figure Set

Analysis bundles

create_analysis_bundle(): Create a Structured Post-Fit Analysis Bundle
analysis_bundle_table(): Analysis-Bundle Status Table
create_publication_table_set(): Extract Publication Tables from an Analysis Bundle
create_analysis_figure_set(): Create Publication Figures from an Analysis Bundle
write_analysis_bundle_report(): Write an Analysis-Bundle Markdown Report

Advanced prediction diagnostics

prediction_draws_long(): Convert Prediction Draws to Long Form
posterior_predictive_statistic(): Posterior Predictive Statistic Check
ppc_statistic_table(): Posterior Predictive Statistic Table
binary_confusion_table(): Binary Confusion Table
binary_roc_curve(): Binary ROC Curve
binary_precision_recall_curve(): Binary Precision-Recall Curve
binary_calibration_error(): Binary Calibration Error
binary_group_calibration(): Grouped Binary Calibration
duration_qq_table(): Duration Predictive Q-Q Table
duration_tail_check(): Duration Tail Check
group_prediction_summary(): Group Prediction Summary
prediction_pairwise_contrasts(): Pairwise Prediction Contrasts
prediction_interval_width(): Prediction Interval Width Table
prediction_rank_probabilities(): Posterior Ranking Probabilities for Prediction Rows
plot_prediction_draws(): Prediction-Draw Distribution Plot
plot_ppc_statistic(): Posterior Predictive Statistic Plot
plot_binary_roc(): Binary ROC Plot
plot_binary_precision_recall(): Binary Precision-Recall Plot
plot_binary_group_calibration(): Grouped Binary Calibration Plot
plot_duration_qq(): Duration Predictive Q-Q Plot
plot_duration_tail(): Duration Tail-Check Plot
plot_group_predictions(): Group Prediction Plot
plot_prediction_interval_width(): Prediction Interval-Width Plot
plot_prediction_rank_probabilities(): Prediction Rank-Probability Plot

Evidence graphics and reporting

sensitivity_suite_table(): Sensitivity-Suite Table
model_evidence_table(): Model-Evidence Table
backend_parity_table(): Backend-Parity Table
backend_environment_table(): Backend-Environment Table
manifest_comparison_table(): Manifest-Comparison Table
schema_comparison_table(): Schema-Comparison Table
design_support_table(): Design-Support Table
missingness_audit_table(): Missingness-Audit Table
plot_sensitivity_suite_gg(): Plot a Sensitivity Suite with ggplot2
plot_model_evidence_gg(): Plot Model-Evidence Availability with ggplot2
plot_backend_parity_gg(): Plot Backend Parity with ggplot2
plot_backend_environment_gg(): Plot Backend Environment Checks with ggplot2
plot_manifest_comparison_gg(): Plot Manifest Differences with ggplot2
plot_schema_comparison_gg(): Plot Schema Differences with ggplot2
plot_design_support_gg(): Plot Design-Support Components with ggplot2
plot_missingness_gg(): Plot Missingness Fractions with ggplot2
create_model_card(): Create a gp3bayes Model Card
model_card_table(): Model-Card Evidence Table
create_reporting_checklist(): Create a Reporting Checklist
plot_reporting_checklist(): Plot a Reporting Checklist
write_model_card(): Write a Model Card

Recovery, sensitivity, and SBC publication

recovery_parameter_table(): Recovery Parameter Summary Table
recovery_estimate_table(): Recovery Estimate Table
recovery_fit_status_table(): Recovery Fit-Status Table
prior_sensitivity_table(): Prior Sensitivity Table
prior_sensitivity_scenario_table(): Prior Sensitivity Scenario Table
estimand_sensitivity_table(): Estimand Sensitivity Table
group_deletion_sensitivity_table(): Group-Deletion Sensitivity Table
random_slope_sensitivity_table(): Random-Slope Sensitivity Table
powerscale_sensitivity_table(): Power-Scale Sensitivity Table
sbc_stats_table(): SBC Statistics Table
sbc_overview_table(): SBC Overview Table
plot_recovery_bias(): Plot Recovery Standardized Bias
plot_recovery_coverage(): Plot Recovery Coverage
plot_recovery_rmse(): Plot Recovery RMSE
plot_recovery_estimates(): Plot Repetition-Level Recovery Estimates
plot_recovery_fit_status(): Plot Recovery Fit Status
plot_prior_sensitivity(): Plot Prior-Scale Sensitivity
plot_prior_sensitivity_scenarios(): Plot Prior-Sensitivity Scenario Maxima
plot_estimand_sensitivity_gg(): Plot Estimand Sensitivity with ggplot2
plot_group_deletion_sensitivity(): Plot Group-Deletion Sensitivity
plot_random_slope_sensitivity(): Plot Random-Slope Sensitivity
plot_powerscale_sensitivity_gg(): Plot Power-Scale Sensitivity with ggplot2
plot_sbc_rank_gg(): SBC Rank-Histogram Plot
plot_sbc_ecdf_gg(): SBC ECDF-Difference Plot
plot_sbc_coverage_gg(): SBC Coverage Plot
plot_sbc_simulated_vs_estimated_gg(): SBC Simulated-versus-Estimated Plot

Prior-posterior and LOO evidence atlases

prior_specification_table(): Prior-Specification Table
simulate_declared_prior_draws(): Simulate Marginal Draws from Declared gp3bayes Priors
prior_posterior_bridge(): Create a Declared-Prior versus Posterior Bridge
prior_posterior_summary_table(): Prior-versus-Posterior Summary Table
prior_posterior_distance_table(): Prior-versus-Posterior Distance Table
prior_posterior_draws_long(): Long Prior and Posterior Draw Table
plot_prior_posterior_density(): Plot Declared Prior and Posterior Densities
plot_prior_posterior_intervals(): Plot Prior and Posterior Intervals
plot_prior_posterior_shift(): Plot Prior-to-Posterior Location Shift
plot_prior_posterior_contraction(): Plot Prior-to-Posterior Contraction
loo_pointwise_table(): Pointwise LOO Table
loo_influence_summary(): LOO Influence Summary
loo_flagged_data(): Flagged LOO Observation Data
create_loo_influence_atlas(): Create a LOO Influence Atlas
loo_influence_atlas_table(): LOO Influence Atlas Table
plot_loo_pointwise_elpd(): Plot Pointwise LOO ELPD
plot_loo_pareto_vs_elpd(): Plot Pareto-k versus Pointwise ELPD
plot_loo_influence_rank(): Plot Ranked LOO Influence

Publication registry and diagnostic dashboard

create_publication_registry(): Create a Publication Registry
register_publication_table(): Register a Publication Table
register_publication_figure(): Register a Publication Figure
publication_registry_table(): Publication Registry Table
validate_publication_registry(): Validate a Publication Registry
write_publication_registry(): Write a Publication Registry
save_publication_registry_figures(): Save Publication Registry Figures
create_complete_evidence_inventory(): Create a Complete Evidence Inventory
evidence_inventory_table(): Evidence Inventory Table
create_diagnostic_dashboard(): Create a Diagnostic Dashboard Object
diagnostic_dashboard_table(): Diagnostic Dashboard Table
create_diagnostic_dashboard_figures(): Create Diagnostic Dashboard Figures
plot_diagnostic_dashboard(): Plot Diagnostic Dashboard Availability
write_diagnostic_dashboard_report(): Write a Diagnostic Dashboard Report

Hierarchical effect diagnostics

group_effect_draws_table(): Group-Level Posterior Draw Table
group_effect_rank_probability_table(): Group-Level Rank-Probability Table
random_intercept_variance_partition(): Random-Intercept Latent Variance Partition
random_intercept_variance_partition_table(): Random-Intercept Variance-Partition Table
plot_group_effect_distribution(): Plot Group-Effect Posterior Distributions
plot_group_effect_rank_probability(): Plot Group-Effect Rank Probabilities
plot_random_intercept_variance_partition(): Plot Random-Intercept Variance Partition

Prediction profiles and surfaces

create_prediction_profile(): Create a Numeric Prediction Profile
prediction_profile_table(): Prediction Profile Table
prediction_gradient_table(): Prediction-Profile Gradient Table
plot_prediction_profile(): Plot a Prediction Profile
plot_prediction_gradient(): Plot Prediction-Profile Gradients
create_prediction_surface(): Create a Two-Dimensional Prediction Surface
prediction_surface_table(): Prediction Surface Table
plot_prediction_surface(): Plot a Prediction Surface
plot_prediction_surface_uncertainty(): Plot Prediction-Surface Uncertainty
create_prediction_contrast_profile(): Create a Prediction Contrast Profile
prediction_contrast_profile_table(): Prediction Contrast Profile Table
plot_prediction_contrast_profile(): Plot a Prediction Contrast Profile

Predictive distribution and calibration uncertainty

create_predictive_distribution_atlas(): Create a Posterior-Predictive Distribution Atlas
predictive_distribution_atlas_table(): Predictive Distribution Atlas Table
predictive_quantile_envelope(): Posterior-Predictive Quantile Envelope
prediction_score_uncertainty(): Posterior Uncertainty in Prediction Scores
prediction_score_uncertainty_table(): Prediction Score-Uncertainty Table
binary_calibration_uncertainty(): Binary Calibration Uncertainty
binary_calibration_uncertainty_table(): Binary Calibration-Uncertainty Table
plot_predictive_atlas_statistics(): Plot Predictive Atlas Statistics
plot_predictive_quantile_envelope(): Plot Posterior-Predictive Quantile Envelope
plot_prediction_score_uncertainty(): Plot Prediction Score Uncertainty
plot_binary_calibration_uncertainty(): Plot Binary Calibration Uncertainty

Grouped predictive influence

loo_group_influence_table(): Aggregate LOO Influence by a Declared Group
plot_loo_group_influence(): Plot Grouped LOO Influence
plot_loo_group_elpd(): Plot Grouped Pointwise ELPD Contribution

Pupil contracts, Gazepoint, simulation, and preparation

create_pupil_contract(): Create a governed pupil-timecourse contract
as.data.frame(<gp3bayes_pupil_contract>): Convert a pupil contract to a transparent table
inspect_gazepoint_pupil_schema(): Inspect verified Gazepoint pupil and gaze fields
gazepoint_pupil_mapping_table(): Return the Gazepoint pupil mapping audit table
simulate_pupil_timecourse(): Simulate deterministic hierarchical pupil time courses
prepare_pupil_timecourse(): Prepare a pupil time course under explicit transformations
audit_pupil_readiness(): Audit pupil-timecourse readiness
pupil_readiness_table(): Extract pupil readiness tables
audit_pupil_measurement_context(): Audit pupil measurement and confound context
pupil_measurement_audit_table(): Extract a pupil measurement-context table

Pupil model fitting, prediction, and estimands

specify_pupil_timecourse_model(): Specify the restricted hierarchical pupil time-course model
pupil_specification_table(): Convert a pupil specification to a publication-ready table
translate_pupil_model_to_brms(): Translate an approved pupil model to brms
check_pupil_prior_predictive(): Check the approved pupil priors predictively
fit_pupil_model_backend(): Fit the restricted pupil time-course model with an approved backend
fit_pupil_model(): Fit a pupil model through the fixed rstan route
fit_pupil_model_cmdstanr(): Fit a pupil model through the fixed cmdstanr route
as_pupil_prediction_draws(): Create a lightweight pupil prediction object from frozen draws
predict_pupil_trajectory(): Predict governed pupil trajectories
estimate_pupil_trajectory(): Estimate posterior pupil trajectories
pupil_trajectory_table(): Convert a pupil trajectory to a table
estimate_pupil_window(): Estimate a declared-window mean pupil response
estimate_pupil_auc(): Estimate area under a declared pupil-response window
estimate_pupil_peak(): Estimate posterior peak pupil response inside a declared window
estimate_pupil_peak_latency(): Estimate posterior peak latency inside a declared window
pupil_condition_contrast(): Estimate a posterior condition-difference trajectory
as.data.frame(<gp3bayes_pupil_estimand>): Convert a pupil estimand to a data frame

Pupil diagnostics, validation, and sensitivity

diagnose_pupil_fit(): Diagnose temporal and sampling behaviour of a pupil fit
pupil_residual_acf(): Summarise residual autocorrelation for a pupil fit
check_pupil_posterior_predictive(): Run pupil-specific posterior predictive checks
pupil_ppc_table(): Extract pupil PPC evidence tables
summarise_pupil_posterior(): Summarise a fitted pupil posterior
create_pupil_validation_plan(): Create an explicit pupil predictive-validation plan
validate_pupil_model(): Validate a pupil model for an explicit prediction target
pupil_validation_table(): Extract a pupil validation table
create_pupil_sensitivity_suite(): Create a governed pupil sensitivity suite
materialize_pupil_sensitivity_scenario(): Materialize one declared pupil sensitivity scenario
compare_pupil_sensitivity_estimands(): Compare declared pupil sensitivity estimands
pupil_sensitivity_table(): Extract pupil sensitivity scenarios or comparison results

Pupil publication graphics

plot_pupil_readiness(): Plot pupil readiness evidence
plot_pupil_observed_trajectory(): Plot observed pupil trajectories
plot_pupil_posterior_trajectory(): Plot posterior pupil trajectories or condition differences
plot_pupil_estimand(): Plot declared-window pupil estimands
plot_pupil_ppc(): Plot pupil posterior-predictive evidence
plot_pupil_residual_acf(): Plot pupil residual autocorrelation
plot_pupil_validation(): Plot pupil validation evidence
plot_pupil_sensitivity(): Plot pupil sensitivity scenarios or result comparisons
plot_pupil_measurement_audit(): Plot gaze/PFE and luminance measurement-context evidence

Advanced pupillometry 0.5

Advanced dynamic, robust, measurement-aware, multivariate, predictive, validation, sensitivity, and governance functions introduced in gp3bayes 0.5.

advanced_pupil_trajectory_table(): Summarise an advanced pupil trajectory
audit_advanced_pupil_identifiability(): Audit empirical support for an advanced pupil model specification
audit_binocular_pupil_readiness(): Audit binocular pupil availability and agreement descriptively
audit_pupil_computational_budget(): Audit computational complexity before fitting an advanced pupil model
audit_pupil_measurement_model(): Audit a declared measurement model against data
audit_pupil_missingness(): Audit missingness in an advanced pupil specification
audit_pupil_predictive_calibration(): Audit posterior predictive calibration on explicit evaluation data
audit_pupil_temporal_dependence(): Audit empirical temporal dependence before model fitting
check_advanced_pupil_prior_predictive(): Check advanced pupil priors through prior-only simulation
compare_pupil_autocorrelation(): Compare residual autocorrelation across fitted advanced models
compare_pupil_lfo(): Compare executed leave-future-out validations
compare_pupil_models(): Compare fitted pupil models predictively
create_advanced_pupil_prior_specification(): Create an advanced pupil prior specification
create_pupil_advanced_sensitivity_suite(): Create a pre-fit advanced pupillometry sensitivity suite
create_pupil_arma_spec(): Create an explicit bounded ARMA configuration
create_pupil_gp_spec(): Create a Gaussian-process configuration for pupil trajectories
create_pupil_lfo_plan(): Create an explicit leave-future-out validation plan
create_pupil_measurement_model(): Create a governed measurement-uncertainty specification
create_pupil_missingness_spec(): Create a governed missingness specification
create_pupil_model_set(): Create a named set of fitted pupil models
diagnose_advanced_pupil_fit(): Diagnose an advanced pupil fit
estimate_binocular_pupil_trajectory(): Estimate joint binocular posterior trajectories
estimate_pupil_dynamic_contrast(): Estimate a dynamic posterior contrast between two pupil conditions
estimate_pupil_residual_scale(): Estimate the residual-scale trajectory from a distributional model
estimate_pupil_response_parameters(): Estimate nonlinear response-shape parameters
estimate_pupil_threshold_duration(): Estimate posterior duration above a prespecified dynamic threshold
estimate_pupil_trajectory_derivative(): Estimate posterior temporal derivatives of a pupil trajectory
fit_advanced_pupil_model(): Fit an advanced pupil model using rstan
fit_advanced_pupil_model_backend(): Fit an advanced pupil model through an approved brms backend
fit_advanced_pupil_model_cmdstanr(): Fit an advanced pupil model using cmdstanr
fit_binocular_pupil_model(): Fit a joint binocular pupil model
fit_pupil_response_shape_model(): Fit the experimental nonlinear response-shape model
materialize_pupil_advanced_sensitivity_scenario(): Materialize one advanced sensitivity scenario
plot_advanced_pupil_simulation(): Plot simulated advanced pupil trajectories
plot_advanced_pupil_trajectory(): Plot an advanced posterior pupil trajectory
plot_binocular_pupil_trajectory(): Plot binocular posterior trajectories
plot_pupil_autocorrelation_comparison(): Plot residual autocorrelation comparison
plot_pupil_dynamic_contrast(): Plot a dynamic pupil condition contrast
plot_pupil_gp_hyperparameters(): Plot Gaussian-process hyperparameters
plot_pupil_identifiability_audit(): Plot advanced identifiability/design-support audit
plot_pupil_lfo(): Plot leave-future-out scores
plot_pupil_measurement_uncertainty(): Plot measurement-uncertainty audit
plot_pupil_missingness(): Plot missing-response fraction over time
plot_pupil_model_comparison(): Plot predictive model comparison
plot_pupil_model_complexity(): Plot advanced model computational complexity
plot_pupil_predictive_calibration(): Plot posterior predictive calibration
plot_pupil_residual_scale(): Plot posterior residual scale over time
plot_pupil_residual_spectrum(): Plot residual spectrum
plot_pupil_response_parameters(): Plot experimental nonlinear response parameters
plot_pupil_temporal_dependence(): Plot empirical temporal-dependence audit
plot_pupil_trajectory_derivative(): Plot posterior pupil trajectory derivative
predict_advanced_pupil_trajectory(): Predict an advanced pupil trajectory
prepare_binocular_pupil_timecourse(): Prepare binocular pupil data without averaging eyes
pupil_advanced_capabilities(): Report the gp3bayes 0.5 advanced-pupillometry capability boundary
pupil_advanced_compatibility_table(): Report governed compatibility rules for 0.5 advanced models
pupil_advanced_mapping_table(): Inspect the resolved 0.5 pupil column mapping
pupil_advanced_specification_table(): Tabulate an advanced pupil model specification
pupil_autocorrelation_table(): Tabulate a temporal-dependence audit
pupil_binocular_agreement_table(): Summarise binocular posterior agreement
pupil_binocular_correlation(): Extract posterior residual binocular correlation
pupil_binocular_difference(): Estimate posterior right-minus-left binocular differences
pupil_distribution_table(): Tabulate a pupil distribution declaration or advanced specification
pupil_dynamic_contrast_table(): Tabulate a dynamic pupil contrast
pupil_gp_hyperparameters(): Extract Gaussian-process hyperparameters
pupil_gp_table(): Tabulate GP hyperparameters
pupil_identifiability_table(): Tabulate advanced pupil identifiability/design-support audit
pupil_measurement_uncertainty_table(): Summarise measurement uncertainty declared in a model
pupil_missingness_table(): Tabulate missingness audit results
pupil_model_card(): Build an auditable advanced pupil model card
pupil_model_card_table(): Tabulate a pupil model card
pupil_model_comparison_table(): Tabulate model comparison
pupil_model_weights(): Compute explicit predictive model weights
pupil_residual_scale_table(): Tabulate posterior residual scale
pupil_residual_spectrum(): Compute a descriptive residual spectrum
pupil_response_parameter_table(): Tabulate nonlinear response parameters
pupil_trajectory_derivative_table(): Tabulate posterior pupil trajectory derivatives
score_pupil_predictions(): Score posterior predictive draws against observed pupil values
simulate_advanced_pupil_timecourse(): Simulate advanced dynamic pupil time courses
simulate_binocular_pupil_timecourse(): Simulate joint binocular pupil traces
simulate_pupil_response_shape(): Simulate data from the experimental nonlinear response-shape family
specify_advanced_pupil_timecourse_model(): Specify an advanced governed pupil time-course model
specify_binocular_pupil_model(): Specify a joint binocular pupil model
specify_pupil_distribution(): Declare an advanced pupil observation distribution
specify_pupil_response_shape_model(): Specify the experimental nonlinear pupil response-shape model
translate_advanced_pupil_model_to_brms(): Translate an advanced pupil model to brms without fitting
translate_binocular_pupil_model_to_brms(): Translate a binocular specification to a brms multivariate formula
translate_pupil_response_shape_to_brms(): Translate the experimental response-shape model to brms
validate_pupil_leave_future_out(): Execute or materialize leave-future-out validation

SCR responsivity sensitivity

estimate_scr_responsivity_bayes(): Bayesian retention-first SCR responsivity summary

Multilevel gaze mediation

Bayesian trial-level mediation with explicit within- and between-participant estimands.

create_mediation_prior_specification() specify_multilevel_gaze_mediation() fit_multilevel_gaze_mediation() check_mediation_convergence() prior_predictive_check_mediation() posterior_predictive_check_mediation() estimate_indirect_effect() estimate_within_indirect_effect() estimate_between_indirect_effect() posterior_indirect_effect() posterior_direct_effect() posterior_total_effect() summarise_multilevel_mediation() plot_indirect_effect_distribution() plot_mediation_posteriors() plot_participant_mediation_effects() compare_multilevel_mediation_models() report_multilevel_gaze_mediation() simulate_multilevel_gaze_mediation() specify_multilevel_serial_gaze_mediation() fit_multilevel_serial_gaze_mediation() posterior_serial_indirect_effect() specify_multilevel_moderated_gaze_mediation() fit_multilevel_moderated_gaze_mediation() posterior_conditional_indirect_effect(): Bayesian Multilevel Gaze Mediation Workflows